Pangenomics in the Mimulus guttatus Species Complex

The field of evolutionary genomics is moving away from single-reference genomes and towards pangenomics. Unlike a single-reference genome, chosen as one ‘representative’ individual from a species, the pangenome reference consists of multiple high-quality reference genomes from a set of individuals. Together, these assemblies aim to capture the entire sequence diversity of a species. By comparing genome assemblies directly or mapping sequencing reads to a pangenome resource, researchers can more readily detect structural variation (such as insertions, deletions, duplications and inversions) as well as gene content variation that would have otherwise been missed or mischaracterised with traditional single-reference approaches. In this issue of Molecular Ecology Resources, Lovell et al. (2025) present a pangenome resource constructed from four chromosome-scale annotated reference genomes of the Mimulus guttatus species complex. They explore genome synteny, structural variation and gene presence–absence across the species, as well as examine recombination rate variation and patterns of nucleotide diversity to understand the role of linked selection during adaptation. Below I discuss their results and highlight broad implications for pangenomic approaches when studying highly divergent lineages.